Freesurfer February 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
83 discussions

[FreeSurfer] Lesion detection at different thresholds
by Krystal Xiwing Yau 18 Apr '24

18 Apr '24

External Email - Use Caution Dear FS experts, I am testing out which threshold works the best for the image. As I tested 0.3 and 0.9, the lesion masks do show the difference but the measurement is the same. Please see below for your information: [cid:abc00aac-cc49-4ef4-9cca-50c4bf72188b] Fig 1. Lesion.mgz with a threshold of 0.3 applied to FLAIR image [cid:7e206b3b-741a-497a-aec8-5bef569267b7] Fig 2. Lesions.mgz with a threshold of 0.7 applied to FLAIR image Do the volume of lesions supposedly different with threshold adjustments? The following code is what I used for running samseg: run_samseg --input $FREESURFER_HOME/${i}.nii $FREESURFER_HOME/${i}_flair_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 --output $SUBJECTS_DIR/${i}_samsegOutput_thold0.7/ --save-posteriors --threads 8 Thank you for your attention. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

4 17

xhemi
by Joost Janssen 06 Mar '24

06 Mar '24

External Email - Use Caution Dear Doug, The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The following commands work without error but are they correct for meeting my objective? Thanks. surfreg --s $subject --t fsaverage_sym --lh --no-annot surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg $subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg $subject/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg $subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg $subject/xhemi/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0 $subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o $subject/surf/li.thickness.lh.fsaverage_sym.mgh mri_segstats --annot fsaverage lh aparc --i $subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum $subject/stats/li.thickness.aparc.stats -joost

2 3

Re: [Freesurfer] recon-all-clinical synthseg error
by fsbuild 04 Mar '24

04 Mar '24

External Email - Use Caution  It could help to know what OS version and what Freesurfer version you are running.  From your path /usr/local/freesurfer it looks like you are running a Freesurfer release, e.g., 7.4.1. - R. On Feb 25, 2024, at 21:45, Agata Wolna <awolna(a)mit.edu> wrote:        External Email - Use Caution        Hi!I'm trying to run recon-all-clinical but I'm running into an error with the SynthSeg at the very beginning. Do you have any hints what the problem might be here? Here's the full error message:the following problem occured with image [mypath]/mri/native.mgz :Traceback (most recent call last):  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in predict    image, aff, h, im_res, shape, pad_idx, crop_idx = preprocess(path_image=path_images[i],  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in preprocess    im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image, True)  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in get_volume_info    im, aff, header = load_volume(path_volume, im_only=False)  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1377, in load_volume    x = nib.load(path_volume)  File "/usr/local/freesurfer/python/lib/python3..8/site-packages/nibabel/loadsave.py", line 110, in load    img = image_klass.from_filename(filename, **kwargs)  File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py", line 503, in from_filename    return klass.from_file_map(file_map, mmap=mmap, keep_file_open=keep_file_open)  File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py", line 526, in from_file_map    header = klass.header_class.from_fileobj(mghf)  File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py", line 171, in from_fileobj    + int(klass._data_type_codes.bytespervox[tp]) * np.prod(hdr_str_to_np['dims'])KeyError: 10resuming program executionERROR: some problems occured for the following inputs (see corresponding errors above):[mypath]/mri/native.mgzError in SynthSegBest,Agata_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 2

mris_convert reading surf.gii files?
by Westin, Karin 04 Mar '24

04 Mar '24

External Email - Use Caution Hi I'm trying to create an .annot file from a label.gii file using an HCP fsavarage.surf.gii file (eg mris_convert --annot my_label.label.gii fsaverage_template.L.surf.gii lh.my_annot.annot). However I keep getting the error ** failed to open GIFTI XML file 'fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii' mrisReadGIFTIdanum: gifti_read_image() returned NULL Is there a better way to read/open CIFTI files using mris_convert? Best and thanks Karin

2 9

Re: [Freesurfer] Subject does not have a bstampfile
by fsbuild 04 Mar '24

04 Mar '24

External Email - Use Caution   Let me add that it will not work to use shared mount point from the Windows filesystem as you list below, /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri - for your SUBJECTS_DIR when running a recon-all command.  The command will fail because the Windows file system does not support soft-links.   Any SUBJECTS_DIR used for recon-all needs to be inside the Linux OS image running freesurfer.  You could however copy the files from that mount point to create another SUBJECTS_DIR somewhere inside your Linux image, e.g., under your home directory in linux. .... in your linux terminal window ... $ cd$ mkdir subjects$ export SUBJECTS_DIR=$HOME/subjects$ cd $SUBJECTS_DIR$ cp -p -f -R /mnt/c/Users/GCM/Desktop/subjects/NowakG . - R. On Jan 8, 2024, at 16:10, Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote:You need to specify the input files to process. Here is the wiki page for recon-all -  https://secure-web.cisco.com/1hqVY7QioPnD85rxOcGMUcCuynnW47DWZwkPX0Z-CZpPZhsuOE3Dqq56yZOR48pnqlARbSGSU1uJNTssTzOLeJZDej-4B4APtXHQmIDTAeNiz6injsGyGghBE4szgzC-CIvlktYVKAeIFD9vBNBZGTgRtRAfcxOZTJJXzk0kPtE9fSY8vo9o05Q8Lf5La4t7Av6IvB6hkO3ZqlfaDGIxlZfRhNJC0f5oWDNXpfp8nYykG-egLh8zOuhOsHSbWCac7UKV67GamZPc5FS5KwH3vo_4_Omj5v0dIRxZ5O4d9WtJGN0f3IkrLaqnXHmnqhmI4YmYtNQmp-0UBF38a-xfw4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-allBest,Yujing-----Original Message-----From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Joanna KidonSent: Monday, January 8, 2024 3:33 PMTo: freesurfer(a)nmr.mgh.harvard.eduSubject: [Freesurfer] Subject does not have a bstampfile       External Email - Use Caution        Hello FreeSurfer Developers,I'm attempting to compute Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal), as described on the https://secure-web.cisco.com/1JRIAQtmLphlXIykU3RsSWy2GeEv_y0Em3hHjyX02njKQR… I get the following error when I run the recon-all -all -s command:Subject does not have a bstampfile, copying /usr/local/freesurfer/7.3.2/build-stamp.txtSubject FS Version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version DoneINFO: SUBJECTS_DIR is /mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux#--------------------------------------------#@# MotionCor Sun Jan  7 20:48:46 CET 2024ERROR: no run data found in/mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume called 001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig.If you have a second run of data call it 002.mgz, etc.See also: http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwu… LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s NowakG exited with ERRORS at Sun Jan  7 20:48:46 CET 2024I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the scripts/recon-all.log in case it's of any use.Best regards,Joanna------------------------------------------------------------------------------------dr n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej Górnośląskie Centrum Medycznego im. prof. L. Gieca SUM w KatowicachPhD, specialist in medical physics, neurobiologist Chairwoman of the Diagnostic Imaging Section of the Polish Society of Medical Physics Department of Invasive Cardiology and Electrocardiology, 3rd Department of Cardiology, Medical University of Silesia in Katowice Head of the Medical Physics Department, Coordinator for Radiological Protection, Deputy Head of the Department of Diagnostic Imaging Leszek Giec Upper-Silesian Medical Centre of the Medical University of Silesia in Katowice_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

Longitudinal Freesurfer in the presence of large tissue defects
by Philip P 04 Mar '24

04 Mar '24

External Email - Use Caution Dear Freesurfer Developers, I am currently running the Longitudinal Pipeline on a cohort with significant portions of brain tissue removed. The obtained base templates overall look reasonable, however, when overlaying the transformed session T1ws and flicking between them, there still are noticeable residual differences. This is not surprising, given the inevitable brain shift after tissue removal, which rigid registration cannot account for. In my search for a non-linear base template option I came across the "Longitudinal FreeSurfer with non-linear subject-specific template improves sensitivity to cortical thinning” ISMRM abstract (https://secure-web.cisco.com/1me4RY0enlek75e3PAqIseSGOO7tfF84eBwPlWXYndHKO5…) as well as related code on Github (https://secure-web.cisco.com/10WRpCPnvc4D9H2TOaZHsTUn0u7cWtVKoReU9EtexFnzvs…) I was wondering whether you could provide insights into what you think the best strategy for obtaining reliable longitudinal cortical thickness measurements in such a dataset. Do you have a feel for whether the Longitudinal Freesurfer processing stream still provides benefits over Cross-Sectional analysis in the presence of large defects? Would you recommend giving the above-mentioned non-linear implementation a shot or were there other reasons the feature has not been implemented yet in the official version? Thanks already in advance! Best Philip

2 4

Is the slice delay of each slice needed for slice time correction with preprocess-sess?
by Maria Hakonen 03 Mar '24

03 Mar '24

External Email - Use Caution Dear all, Have I understood correctly that the slice delay of each slice is not needed when performing slice time correction with preprocess-sess? I am processing an open OASIS fMRI dataset. The dataset has fMRI data in nifti format and JSON files that contain information about the data. In the instructions they say: "Slice timing is included in the JSON when available. Some original DICOM files did not have slice timing info. When slice timing information is unavailable use the ratio TR/#slices." The data is collected with a Siemens scanner. If the slice timing is available it seems to be interleaved: "SliceTiming": [ 1.1025, 0, 1.165, 0.059999999999999998, 1.2250000000000001, 0.1225, 1.2875000000000001, 0.1825, 1.3474999999999999, 0.245, 1.4099999999999999, 0.30499999999999999, 1.47, 0.36749999999999999, 1.5325, 0.42749999999999999, 1.595, 0.48999999999999999, 1.655, 0.55000000000000004, 1.7175, Could I just run slice time correction with the siemens option? Best regards, Maria

2 1

Vertex / voxel lesion symptom mapping
by Martin Juneja 03 Mar '24

03 Mar '24

External Email - Use Caution Greetings FreeSurfer community, I was just wondering if it's possible to perform vertex/voxel lesion symptom mapping (VLSM) using FreeSurfer? In other words, I would like to assess the impact of lesion topography (of course, heterogenous locations across patients) on neurocognitive function in brain tumor patients. I would greatly appreciate any help/response. Thanks!

2 9

Samseg (cross-sectional, longitudinal, MS lesions)
by Krzysztof Barć 01 Mar '24

01 Mar '24

External Email - Use Caution Good morning, 1) For the Samseg protocol, are only T1 and FLAIR sequences required (no MPRAGE scans required)? 2) What does the numerical output of the Samseg calculation look like? Best regards, Krzysztof Barć

2 1

Re: [Freesurfer] Freesurfer Digest, Vol 240, Issue 19
by Li, Shasha,MD,MS,PhD 29 Feb '24

29 Feb '24

??????? ______________________ Shasha Li MD, PhD Assistant Professor, Martinos Center/Radiology (She/her/hers) Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 T 617-642-0449 massgeneral.org ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Thursday, February 29, 2024 5:00:01 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 240, Issue 19 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Support Request NextBrain (Sorby-Adams, Annabel) 2. Re: Longitudinal Freesurfer in the presence of large tissue defects (Philip P) 3. mri_synthseg fails with current model files (was Re: Support Request NextBrain) (fsbuild) 4. Re: [ext] Re: mris_convert reading surf.gii files? (Westin, Karin) 5. Re: [ext] Re: mris_convert reading surf.gii files? (Huang, Yujing) 6. Re: [ext] Re: mris_convert reading surf.gii files? (Westin, Karin) 7. Re: Creating a custom registration template with FreeSurfer template (Huang, Yujing) 8. Re: [ext] Re: mris_convert reading surf.gii files? (Huang, Yujing) 9. Re: [ext] Re: mris_convert reading surf.gii files? (Westin, Karin) 10. Re: [ext] Re: mris_convert reading surf.gii files? (Huang, Yujing) ---------------------------------------------------------------------- Message: 1 Date: Thu, 29 Feb 2024 01:11:25 +0000 From: "Sorby-Adams, Annabel" <ASORBY-ADAMS(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Support Request NextBrain To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: fsbuild <fsbuild(a)contbay.com> Message-ID: <CF02DF80-4A65-4780-85A0-26F4D30B59B4(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Helen, I managed to run mri_synthseg on my M2 Mac by coping over the model file to the 7.3.2 version of freesurfer, and installing the tensorflow workaround previously posted on the forum for apple silicon machines. I have not been able to get it to work on the 7.4 or most recent dev versions unfortunately. The work around for 7.3.2 isn?t ideal, but does the trick. Freesurfer gurus may have more insight though! Annabel On 28 Feb 2024, at 20:03, Friedrich, Helen <hfriedrich(a)bwh.harvard.edu> wrote: ? Hi R, Thanks for your quick response. We actually did that initially and it did not work unfortunately. Could you provide me with segmentations for a certain scan? Or do you see any other possibility to make it work? Best, Helen ______________________ Helen Friedrich, B.Sc. Doctoral Student Netstim Laboratory Center for Brain Circuit Therapeutics Department of Neurology Harvard Medical School Brigham and Women?s Hospital 75 Francis St, Boston MA 02115 brighamandwomens.org <Outlook-rrf3zs4o.png> ________________________________ Von: fsbuild <fsbuild(a)contbay.com> Gesendet: Mittwoch, 28. Februar 2024 17:20 An: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Cc: Friedrich, Helen <hfriedrich(a)bwh.harvard.edu> Betreff: Re: [Freesurfer] Support Request NextBrain External Email - Use Caution The mri_synthseg script and python in the freesurfer disrtibution you are running are not entirely compatible with the arm64 M1, M2, M3 processors in silicon Macs. You could try installing and running the development build of Freesurfer for the silicon Mac via the link below. (After download, right click on the .pkg installer, and select open with default, then follow the prompts). https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS… We would be interested to know if you run into such issues with the above development build. Please keep in mind a development build can be unstable and has not been tested like an actual release. Your numerical result may differ with the development build compared to the previous build/release. - R. On Feb 28, 2024, at 14:25, Friedrich, Helen <hfriedrich(a)bwh.harvard.edu> wrote: Dear Support Team, I'm reaching out for assistance with setting up NextBrain - mri_synthseg. Unfortunately, I could not make it work. There seems to be an issue with the np.float128-section. This error keeps showing up: <image.png> I have also tried to delete np.float128 from the script (as per suggestion from my colleague). However, the same error showed up. I'm working on a macOS M1. I would be very grateful for your assistance. Best, Helen ______________________ Helen Friedrich, B.Sc. Doctoral Student Netstim Laboratory Center for Brain Circuit Therapeutics Department of Neurology Harvard Medical School Brigham and Women?s Hospital 75 Francis St, Boston MA 02115 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be brighamandwomens.org<http://secure-web.cisco.com/17q0ctEVbQ3PCi9RlB5rYtmqkWfH8bL_7IwtwRdv14OcX42…> <Outlook-jaw0jfh4.png> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1rtWoOggy348yAexwX2GFQkliC-8Cc9lypKqh3QJHEwErL…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer February 2024